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The proportions of Denisovan DNA in modern human populations are shown as red in pie charts, relative to New Guinea and Australian Aborigines image based on [1], updated by  [2].

Percentage of Denisovan DNA in modern human populations shown relative to New Guinea and Australian Aborigines. Image based on [3], updated with vegetation and route of modern humans with stars on places where there are homonin finds such as in Flores, Indonesia {Homo floresiensis}, and in Callao, Philippines {currently with unknown homonin affiliation} [5].

In a post almost 3 years ago, I wrote about the ancient connection of the Philippine Negrito groups with indigenous Australians based on [1].  Back then I asked the question, “Is there a link between the archaic hominin from Denisova and these Filipinos?” I anchored my question on a Nature article [2] that says this hominin contributed genes to the ancestors of present day Papuans and Melanesians.

I wasn´t aware that a few months later, some of the researchers involved in [1] and [2] already came up with an answer.

And it was an astounding YES [3]! Why am I writing it just now? Because I wasn´t aware of the paper! I was busy with some other things.*

Here it goes.

The Denisovan is a hominin that is genetically distinct from modern Human and Neanderthal. The hominin derives its name from Denisova Cave in the Altai Mountains in Siberia where a finger bone of this hominin was found. Genetic analyses done to this bone suggest an “unknown type of hominin that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago [4].”

So there you have it. The Neanderthals, the modern Humans, and the Denisovans, and (some other unknown hominins ?) have a common ancestor about a million years ago. These hominins share the same planet at some point in its history, probably even as recent as ~30,000 years ago. 

But what made me think that there might be a connection between the Mamanwas and the Denisovans?

The two research articles [1] and [2] practically scream the question. In [1], the Philippine Negritos have an ancient relation with the Papuans and the Melanesians while in [2], researchers observe Denisova genetic material in current Papuans and the Melanesians. However, it is not that simple as the researchers wrote in [3].

The researchers considered more samples in [3] as it is not only interesting to find the extent of populations with Denisova genetic material but “the presence or absence of Denisova genetic material in particular populations should provide an informative probe for the migration history of Southeast Asia and Oceania.” The researchers sampled genetic materials from an additional 33 populations in South Asia, Southeast Asia and Oceania, including samples from Mamanwa (a Philippine Negrito) and Manobo (a Philippine non-Negrito).

The researchers found that:

  1. There is a significant evidence of Denisova genetic material for the indigenous Australian, the Oceanians and of course in Papuan populations as well as in the Philippine populations considered. However, there is no significant evidence for mainland East Asians, western Negritos (Jehai and Onge), or western Indonesian populations. Being a Negrito does not automatically mean that one has Denisova genetic materials.
  2. The Papuans and Australians have “indistinguishable proportions of Denisovan ancestry (within the statistical error), suggesting Denisova gene flow into the common ancestors of Australians and New Guineans prior to their entry into Sahul (Pleistocene New Guinea and Australia).”
  3. Except for the Philippine and the Australian populations, the Denisova genetic material can be explained by Near Oceanian common ancestry. As seen from the figure below, their fraction of Denisovan ancestry is proportional to their fraction of Near Oceanian ancestry. The Mamanwas, as well as the Manobos, do not follow this one to one correspondence. With further analyses, the researchers say that the Mamanwas and the Manobos do not share common ancestry with the Australians also.
  4. On a later time after the gene flow between modern humans and Denisovans, modern humans that do not have Denisova genetic materials interbred with those with Denisova genetic materials diluting this hominin’s gene proportions further.

The Mamanwa (green triangles) Denisovan material cannot be explained by Near Oceanian gene flow. Image from [1].

The Mamanwa (green triangles) Denisovan material cannot be explained by Near Oceanian gene flow. Image from supplemental pages of [3].

So how did the researchers model population separation and interbreeding based on their findings?

A very simplistic model is presented in the figure below. There was a lot of mixing happening.

This model says non-African modern humans mix with Neandertals and then the ancestors of the Australian, Papuans and Mamanwa populations mix with Denisovans further.

The population with Denisovan genes separated: first the ancestors of Mamanwa, then the separation of the ancestors of Australians and the Papuans.

Before the separation of the ancestors of Australians and the Papuans, however, a population that could be traced from the ancestors of the Onge were able to mix with them.

And finally, the ancestors of the Mamanwas mixed with populations that traces its ancestors to East Asia.

Gene flow graph that shows estimated admixture proportions. Note the divergence of the Mamanwa with the ancestors of the New Guineans and the Australians. Image from [1].

Gene flow graph that shows estimated admixture proportions. The Mamanwa, the New Guineans and the Australians have the same ancestors carrying Denisovan genetic materials. Lengths of the branches do not give information about time. Image from [3].

The researchers based on their results suggest that interbreeding might have occurred in Southeast Asia itself because there was no significant Denisova genetic material found in populations other than the Philippine, Australian and near Oceanian populations.

In [4], Cooper and Stringer “infer that the Denisovans east of the Wallace line (see top figure) may be represented by the Philippines Callao specimen, or have not yet been recognized.” Futher, they said, “Other enigmatic hominin remains in Asia—from Narmada (India) and Dali, Jinniushan, Maba, and Xujiayao (China)—may represent the apparently once more extensive Denisovan population, or perhaps yet other species.”

Genetic and archaeological signatures of Denisovans are widely dispersed – from the Russian Altai mountains, to Australia, to even in Spain where an analysis of a genetic material of a 300,000-year old bone showed that it is closely related to the lineage leading to Denisovans [5].

Cooper and Stringer asked, “Why did gene flow between Denisovans and modern human populations occur primarily east of Wallace’s Line and not on the Asian mainland?”

They said that the first modern human groups, which encountered Denisovan populations, were likely few because of the difficulty of crossing the seas across the Wallace line. The Denisova genetic material then were most likely preserved (not so much diluted?) in the descendants.

But of course the questions of when and where the interbreeding occurred are still open and are waiting for an answer.

The study only considered 2 Philippine ethnolinguistic groups. What could be the Denisova genetic material proportions in other Filipino groups? That would be exciting to see.

*Backpost features significant scientific articles I failed to highlight when they were still “fresh.”  The article in this post in particular, was published when I was preparing to go back to the Philippines from the Netherlands. There will be more back posts in the future I hope.

___________________

References:

[1]  Delfin F, Salvador JM, Calacal GC, Perdigon HB, Tabbada KA, Villamor LP, Halos SC, Gunnarsdóttir E, Myles S, Hughes DA, Xu S, Jin L, Lao O, Kayser M, Hurles ME, Stoneking M, & De Ungria MC (2010). The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups. European journal of human genetics : EJHG PMID: 20877414

[2] Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin JJ, Kelso J, Slatkin M, & Pääbo S (2010). Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature, 468 (7327), 1053-60 PMID: 21179161

[3] Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AM, Ko YC, Jinam TA, Phipps ME, Saitou N, Wollstein A, Kayser M, Pääbo S, & Stoneking M (2011). Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. American journal of human genetics, 89 (4), 516-28 PMID: 21944045

[4] Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, & Pääbo S (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature, 464 (7290), 894-7 PMID: 20336068

[5] Cooper A, & Stringer CB (2013). Paleontology. Did the Denisovans cross Wallace’s Line? Science (New York, N.Y.), 342 (6156), 321-3 PMID: 24136958

[6] Meyer, M, Fu, Q, Aximu-Petri, A, Glocke, I, Nickel, B, Arsuaga, JL, Martinez, I, Gracia, A, de Castro, JMB, Carbonell, E, & Paabo, S (2013). A mitochondrial genome sequence of a hominin from Sima de los Huesos Nature DOI: 10.1038/nature12788

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